Recently upgraded to new gcc7 release, which unfortunately seems to have broken numpy (at least on python2 for sure, did not test python3). Here is a partial traceback showing what happens on import: File "[redacted]", line 16, in <module> import numpy as np File "/usr/lib64/python2.7/site-packages/numpy/__init__.py", line 142, in <module> from . import add_newdocs File "/usr/lib64/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module> from numpy.lib import add_newdoc File "/usr/lib64/python2.7/site-packages/numpy/lib/__init__.py", line 19, in <module> from .polynomial import * File "/usr/lib64/python2.7/site-packages/numpy/lib/polynomial.py", line 20, in <module> from numpy.linalg import eigvals, lstsq, inv File "/usr/lib64/python2.7/site-packages/numpy/linalg/__init__.py", line 51, in <module> from .linalg import * File "/usr/lib64/python2.7/site-packages/numpy/linalg/linalg.py", line 30, in <module> from numpy.linalg import lapack_lite, _umath_linalg ImportError: libgfortran.so.3: cannot open shared object file: No such file or directory I do have the fortran USE flag enabled. Reverting to =sys-devel/gcc-6.4.0 resolves the problem. Reproducible: Always Steps to Reproduce: # USE=fortran emerge =sys-devel/gcc-7.2.0 $ python2 >>> import numpy as np Actual Results: See traceback above. Expected Results: numpy import should complete without errors. Portage 2.3.15 (python 3.6.3-final-0, hardened/linux/amd64, gcc-6.4.0, glibc-2.26-r3, 4.14.1-gentoo x86_64) ================================================================= System uname: Linux-4.14.1-gentoo-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T5850_@_2.16GHz-with-gentoo-2.4.1 KiB Mem: 3065764 total, 1273428 free KiB Swap: 7864316 total, 7863540 free Timestamp of repository gentoo: Tue, 21 Nov 2017 15:22:31 +0000 Head commit of repository gentoo: b69b22665ef347e53e38facce3b31184ec3051d4 sh bash 4.4_p12 ld GNU ld (Gentoo 2.29.1 p2) 2.29.1 app-shells/bash: 4.4_p12::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.26.1-r1::gentoo dev-lang/python: 2.7.14-r1::gentoo, 3.6.3-r1::gentoo dev-util/cmake: 3.9.6::gentoo dev-util/pkgconfig: 0.29.2::gentoo sys-apps/baselayout: 2.4.1-r2::gentoo sys-apps/openrc: 0.34.9::gentoo sys-apps/sandbox: 2.12::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r4::gentoo sys-devel/automake: 1.15.1-r1::gentoo sys-devel/binutils: 2.29.1-r1::gentoo sys-devel/gcc: 6.4.0::gentoo sys-devel/gcc-config: 1.9.0::gentoo sys-devel/libtool: 2.4.6-r4::gentoo sys-devel/make: 4.2.1-r1::gentoo sys-kernel/linux-headers: 4.13::gentoo (virtual/os-headers) sys-libs/glibc: 2.26-r3::gentoo Repositories: gentoo location: /usr/portage sync-type: git sync-uri: https://github.com/gentoo-mirror/gentoo priority: -1000 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php7.0/ext-active/ /etc/php/cgi-php7.0/ext-active/ /etc/php/cli-php7.0/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-O2 -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync multilib-strict news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" PORTAGE_TMPDIR="/var/tmp" USE="acl amd64 berkdb bzip2 cli cracklib crypt cxx dri gdbm hardened iconv ipv6 justify modules multilib ncurses nls nptl openmp pam pcre pie readline seccomp session ssl ssp tcpd unicode urandom xattr xtpax zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-0" POSTGRES_TARGETS="postgres9_5" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python3_6 python2_7" RUBY_TARGETS="ruby22" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, MAKEOPTS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
(In reply to matoro from comment #0) > Here is a partial traceback showing what happens on import: Partial? Why partial? > Steps to Reproduce: > # USE=fortran emerge =sys-devel/gcc-7.2.0 Do you mean that you didn't try rebuilding numpy? (In reply to matoro from comment #0)
There was another similar report, but for arpack yesterday (https://bugs.gentoo.org/638384). The problem is that gfortran from gcc-7 produce libgfortran.so.4, which is a bump from previous version of gcc that had been on .so.3 for a long time. Your blas/lapack has been compiled with a previous version that linked to libgfortran.so.3. You need to rebuild blas and lapack and then probably all their dependencies. This is quite unfortunate.
(In reply to Jeroen Roovers from comment #1) > (In reply to matoro from comment #0) > > Here is a partial traceback showing what happens on import: > > Partial? Why partial? > > > Steps to Reproduce: > > # USE=fortran emerge =sys-devel/gcc-7.2.0 > > Do you mean that you didn't try rebuilding numpy? > > > > (In reply to matoro from comment #0) No, I did try rebuilding numpy. It did not change the results. I will try rebuilding blas, lapack and dependencies and report back.
May be a message similar to the one for gcc-5 about the C++ abi should be considered for gcc-7 about gfortran. The equivalent command to run would be revdep-rebuild --library 'libgfortran.so.3' -- --exclude gcc
Rebuilding blas and lapack with --emptytree seemed to work. Closing this bug for now, thank you for the help.
